Data Quality Assessment Report

massqc from tidymass by Xiaotao Shen

2022-01-16

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INTRODUCTION

massqc (version 0.01): Created in 2021 by Xiaotao Shen

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PARAMETERS

Table 1: Parameter setting

pacakge_name	function_name	parameter	time
massdataset	create_mass_dataset()	no:no	2022-01-16 16:19:04
massprocesser	process_data	path:mzxml_ms1_data/POS	2022-01-16 16:18:43
massprocesser	process_data	polarity:positive	2022-01-16 16:18:43
massprocesser	process_data	ppm:10	2022-01-16 16:18:43
massprocesser	process_data	peakwidth:10,60	2022-01-16 16:18:43
massprocesser	process_data	snthresh:10	2022-01-16 16:18:43
massprocesser	process_data	prefilter:3,500	2022-01-16 16:18:43
massprocesser	process_data	fitgauss:FALSE	2022-01-16 16:18:43
massprocesser	process_data	integrate:2	2022-01-16 16:18:43
massprocesser	process_data	mzdiff:0.01	2022-01-16 16:18:43
massprocesser	process_data	noise:500	2022-01-16 16:18:43
massprocesser	process_data	threads:4	2022-01-16 16:18:43
massprocesser	process_data	binSize:0.025	2022-01-16 16:18:43
massprocesser	process_data	bw:5	2022-01-16 16:18:43
massprocesser	process_data	output_tic:FALSE	2022-01-16 16:18:43
massprocesser	process_data	output_bpc:FALSE	2022-01-16 16:18:43
massprocesser	process_data	output_rt_correction_plot:FALSE	2022-01-16 16:18:43
massprocesser	process_data	min_fraction:0.5	2022-01-16 16:18:43
massprocesser	process_data	fill_peaks:FALSE	2022-01-16 16:18:43
massdataset	mutate()	parameter_1:batch=as.character(batch)	2022-01-16 23:41:16

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SAMPLE INFORMATION

#> -------------------- 
#> massdataset version: 0.99.1 
#> -------------------- 
#> 1.expression_data:[ 10149 x 259 data.frame]
#> 2.sample_info:[ 259 x 6 data.frame]
#> 3.variable_info:[ 10149 x 3 data.frame]
#> 4.sample_info_note:[ 6 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2022-01-16 16:19:04
#> process_data ---------- 
#>         Package Function.used                Time
#> 1 massprocesser  process_data 2022-01-16 16:18:43
#> mutate ---------- 
#>       Package Function.used                Time
#> 1 massdataset      mutate() 2022-01-16 23:41:16

Figure 1: Peak intensity profile.

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MISSING VALUES

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MISSING VALUES IN DATASET

Black is MV.

Figure 2: Missing values in dataset

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MISSING VALUES IN VARIABLES

Figure 3: Missing values in variables

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MISSING VALUES IN SAMPLES

Figure 4: Missing values in samples

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RSD DISTRIBUTATION

Figure 5: RSD distributation

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INTENSITY FOR ALL THE VARIABLES

Figure 6: Intensity for all the variables

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SAMPLE CORRELATION

Figure 7: Sample correlation

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PCA score plot

Figure 7: PCA score plot